Merge pull request #73 from fmalmeida/dev

Wrap-up version 3.2.0

.github/workflows/test_pr_hybrid_docker.yml

@@ -0,0 +1,37 @@
+name: Testing hybrid / docker from PR
+on:
+  pull_request:
+    branches: [master, dev]
+    types: [opened, synchronize, reopened]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Check out pipeline code
+      uses: actions/checkout@v2
+
+    - name: Install Nextflow
+      env:
+        CAPSULE_LOG: none
+      run: |
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+
+    - name: Clean environment
+      run: |
+        sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+        sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+    - name: Run tests for hybrid
+      run: |
+        nextflow run main.nf -profile docker,test,hybrid,pacbio --skip_haslr
+        rm -r work .nextflow*
+
+    - name: View results
+      run: |
+        sudo apt-get install -y tree
+        tree hybrid_test_pacbio

.github/workflows/test_pr_hybrid_singularity.bkp

@@ -0,0 +1,42 @@
+name: Testing hybrid / singularity from PR
+on:
+  pull_request:
+    branches: [master, dev]
+    types: [opened, synchronize, reopened]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Check out pipeline code
+      uses: actions/checkout@v2
+
+    - name: Install Singularity
+      uses: eWaterCycle/setup-singularity@v7
+      with:
+        singularity-version: 3.8.3
+
+    - name: Install Nextflow
+      env:
+        CAPSULE_LOG: none
+      run: |
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+
+    - name: Clean environment
+      run: |
+        sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+        sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+    - name: Run tests for hybrid
+      run: |
+        nextflow run main.nf -profile singularity,test,hybrid,pacbio
+        rm -r work .nextflow*
+
+    - name: View results
+      run: |
+        sudo apt-get install -y tree
+        tree hybrid_test

.github/workflows/test_pr_illumina_docker.yml

@@ -0,0 +1,37 @@
+name: Testing illumina / docker from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for illumina
+        run: |
+          nextflow run main.nf -profile docker,test,sreads
+          rm -r work .nextflow*
+      
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree sreads_test

.github/workflows/test_pr_illumina_singularity.yml

@@ -0,0 +1,42 @@
+name: Testing illumina / singularity from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for illumina
+        run: |
+          nextflow run main.nf -profile singularity,test,sreads
+          rm -r work .nextflow*
+      
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree sreads_test

.github/workflows/test_pr_lreads_docker_ont.yml

@@ -0,0 +1,37 @@
+name: Testing long-reads / docker (ONT) from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for long-reads (ont)
+        run: |
+          nextflow run main.nf -profile docker,test,lreads,ont --max_memory '6.GB' --max_cpus 2 --skip_flye --skip_canu
+          rm -r work .nextflow*
+      
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree lreads_test_ont

.github/workflows/test_pr_lreads_docker_ont_hifi.bkp

@@ -0,0 +1,37 @@
+name: Testing long-reads HIFI / docker (ONT) from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for long-reads (ont)
+        run: |
+          nextflow run main.nf -profile docker,test,lreads,ont_hifi --max_memory '6.GB' --max_cpus 4
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree lreads_test_ont_hifi

.github/workflows/test_pr_lreads_singularity_ont.bkp

@@ -0,0 +1,48 @@
+name: Testing long-reads / singularity (ONT) from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: macos-latest
+
+    steps:
+
+      - name: 'Set up latest Oracle JDK 17'
+        uses: oracle-actions/setup-java@v1
+        with:
+          website: oracle.com
+          release: 17
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for long-reads (ont)
+        run: |
+          nextflow run main.nf -profile singularity,test,lreads,ont
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree lreads_test_ont

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline

.readthedocs.yml

@@ -9,20 +9,12 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.9"
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/conf.py
+mkdocs:
+  configuration: mkdocs.yml
 
-# Build documentation with MkDocs
-# mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
-
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally declare the Python requirements required to build your docs
 python:
   install:
-    - requirements: docs/requirements.txt
+  - requirements: docs/requirements.txt

.zenodo.json

@@ -2,7 +2,7 @@
     "description": "<p>MpGAP is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that adopts well known software for _de novo_ genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes.</p>",
     "license": "other-open", 
     "title": "fmalmeida/MpGAP: A generic multi-platform genome assembly pipeline", 
-    "version": "v3.1.4", 
+    "version": "v3.2", 
     "upload_type": "software",
     "creators": [
         {